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Methodology for determining the linkage and effect of viability genes in selfing organisms (both intragametophytic and regular selfing) is developed. The maximum likelihood estimate of the recombination fraction and the selective effect is determined using a progeny array from a heterozygous parent. The method of lod scores, commonly used in human genetics, is applied to this situation. An example from Scots pine is given and the effect of polyembryony and segregation distortion are discussed.

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